Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#3618 closed defect (duplicate)

vseries problems

Reported by: mmaldo@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-23)
Description
Hi,
I've been getting a number of errors regarding the vseries command, mostly to do wit IndexError: list index out of range. I have a series of 20 volumes. I'm not sure if this is a bug or if I'm not understanding the command properly. When I type "vseries play #1" I get no volume series specified, even though my volume series is #1 (#1.1-#1.20). Thank you.

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/mmaldo/Desktop/chimerax/200805 Session 39 3DVA-Rieske.cxs"
> format session

Summary of feedback from opening /Users/mmaldo/Desktop/chimerax/200805 Session
39 3DVA-Rieske.cxs  
---  
warnings | restore_snapshot for "Volume" returned None  
restore_snapshot for "VolumeSurface" returned None  
notes | Error opening map "/Users/mmaldo/Desktop/chimerax/200805 Session 39
3DVA-Rieske.cxs": File 200805 Session 39 3DVA-Rieske.cxs, format mrc  
MRC header value nsymbt (-1334377196) is invalid  
  
opened ChimeraX session  
Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>  
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree  
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]  
IndexError: list index out of range  
  
Error processing trigger "new frame":  
IndexError: list index out of range  
  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree  
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]  
  
See log for complete Python traceback.  
  

> open
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_019.mrc

Opened FeS_frame_019.mrc, grid size 256,256,256, pixel 1.67, shown at level
0.963, step 1, values float32  
Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 158, in <lambda>  
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree  
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]  
IndexError: list index out of range  
  
Error processing trigger "new frame":  
IndexError: list index out of range  
  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/model_panel/tool.py", line 203, in _fill_tree  
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]  
  
See log for complete Python traceback.  
  

> close session

> open
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_000.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_019.mrc

Opened FeS_frame_000.mrc, grid size 256,256,256, pixel 1.67, shown at level
0.985, step 1, values float32  

> open
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/Vr_CIII2_fit_FeS_Ec1_QQ_nolipids-v2.pdb

Chain information for Vr_CIII2_fit_FeS_Ec1_QQ_nolipids-v2.pdb #2  
---  
Chain | Description  
A M | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G S | No description available  
H | No description available  
J V | No description available  
K | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
W | No description available  
  

> open
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/Vr_CIII2_fit_Qc1_EQ_nolipids-v2.pdb

Chain information for Vr_CIII2_fit_Qc1_EQ_nolipids-v2.pdb #3  
---  
Chain | Description  
A M | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G S | No description available  
H | No description available  
J V | No description available  
K | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
W | No description available  
  

> volume #1.1 level 1.106

> volume #1.1 level 2.227

> volume #1.1 level 2.1

> volume #1.2 level 2.1

> hide atoms

> show cartoons

> color sequential #1-2/A-K chains palette paired-10

> color sequential #2-3/A-K chains palette paired-10

> color sequential #2-3/M-W chains palette paired-10

> hide #!1 models

> show :hem :hec :hea :fes :zn :mg atoms

> color byhetero

Expected a keyword  

> select :hem :hec :hea :fes :zn :mg

536 atoms, 568 bonds, 48 pseudobonds, 4 models selected  

> color sel byhetero

> select clear

> hide #!2 models

> show #!2 models

> hide #!3 models

> view

> morph #2,3

Computed 21 frame morph #4  

> coordset #4 1,21

> morph #2,3

Computed 21 frame morph #5  

> coordset #5 1,21

> movie record

> movie encode /Users/mmaldo/Desktop/movie.mp4 framerate 25.0

Movie saved to /Users/mmaldo/Desktop/movie.mp4  
  

> hide cartoons

> ui mousemode rightMode select

> hide sel atoms

> hide sel atoms

> show #1-2/C,D,Q cartoons

> close #4

> close #5

> show #!2 models

> show #!3 models

> hide sel atoms

> select up

74 atoms, 64 bonds, 4 pseudobonds, 4 models selected  

> select up

266 atoms, 284 bonds, 4 pseudobonds, 4 models selected  

> hide sel atoms

> morph #2,3

Computed 21 frame morph #4  

> coordset #4 1,21

> save session "/Users/mmaldo/Desktop/chimerax/200806 Session 41 Rieske
> morphs.cxs"

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #1.1 level 2

> volume #1.2 level 2

> volume #1.1 level 1.8

> turn y 180

> turn y 180

> turn y 90

> turn y 90

> turn y 90

> turn y 90

> volume #1.1 level 2

> volume #1.1 level 1.8

> volume #1.2 level 1.8

> turn y 10

> turn y -20

> turn y 15

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> cofr #2/Q

> cofr #2/Q

> show #!1 models

> view

> view name front-full-CIII2

> select #1.1

2 models selected  

> select clear

> ui mousemode rightMode translate

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> view name Rieske-zoom

> view front-full-CIII2

> view Rieske-zoom

> hide #!1 models

> open
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_001.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_002.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_003.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_004.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_005.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_006.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_007.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_008.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_009.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_010.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_011.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_012.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_013.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_014.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_015.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_016.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_017.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_018.mrc

Opened FeS_frame_001.mrc, grid size 256,256,256, pixel 1.67, shown at level
0.983, step 1, values float32  

> close #5

> close #1

> open
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_000.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_001.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_002.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_003.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_004.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_005.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_006.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_007.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_008.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_009.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_010.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_011.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_012.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_013.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_014.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_015.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_016.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_017.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_018.mrc
> /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_019.mrc

Opened FeS_frame_000.mrc, grid size 256,256,256, pixel 1.67, shown at level
0.985, step 1, values float32  

> volume #1.1 level 1.8

> volume #1.2 level 1.8

> volume #1.5 level 1.8

> volume #1.4 level 1.8

> volume #1.3 level 1.8

> volume #1.6 level 1.8

> volume #1.7 level 1.8

> volume #1.8 level 1.8

> volume #1.10 level 1.8

> volume #1.11 level 1.8

> volume #1.12 level 1.8

> volume #1.13 level 1.8

> volume #1.15 level 1.8

> volume #1.16 level 1.8

> volume #1.14 level 1.8

> volume #1.17 level 1.8

> volume #1.18 level 1.8

> volume #1.19 level 1.8

> volume #1.20 level 1.8

> volume #1.20 level 2.923

> volume #1.20 level 1.8

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.4 models

> hide #!1.3 models

> hide #!1.5 models

> hide #!1.6 models

> hide #!1.7 models

> hide #!1.8 models

> hide #!1.9 models

> hide #!1.10 models

> hide #!1.11 models

> hide #!1.12 models

> hide #!1.13 models

> hide #!1.14 models

> hide #!1.15 models

> hide #!1.16 models

> hide #!1.17 models

> hide #!1.18 models

> hide #!1.19 models

> hide #!1.20 models

> show #!1.20 models

> hide #!1.20 models

> hide #!1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.1 models

> show #!1.20 models

> hide #!1.1 models

> hide #!4 models

> vseries play #1

No volume series specified  

> vseries play #1.1-1.20

No volume series specified  

> vseries play #1 loop true

No volume series specified  

> vseries play #1

No volume series specified  

> vseries play #1.1

No volume series specified  

> vseries play #1.1,1.20

No volume series specified  

> vseries play #1.1

No volume series specified  

> vseries play #1.1-1.20

No volume series specified  

> vseries play #1.1-1.20

No volume series specified  

Missing or invalid "series" argument: invalid map series specifier  

> vseries save #1 Rieske threshold 1.8

Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/series/vseries_command.py", line 189, in vseries_save  
s = series[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/series/vseries_command.py", line 189, in vseries_save  
s = series[0]  
  
See log for complete Python traceback.  
  

> vseries slider #1

Traceback (most recent call last):  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/series/slider.py", line 142, in play_cb  
self.play()  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/series/slider.py", line 148, in play  
s0 = ser[0]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/series/slider.py", line 148, in play  
s0 = ser[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103
OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Change History (7)

comment:1 by Eric Pettersen, 5 years ago

Cc: Tom Goddard added
Component: Unassigned → Volume Data
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → vseries problems

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Maria,

You should upgrade to the 1.0 release of ChimeraX. I believe all these problems are fixed in 1.0. If you still run into some problems, please report them from the 1.0 version and we will investigate.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by mmaldo@…, 5 years ago 

Hello,

It seems the issue was related to the cryoSparc volume series not recognized as a series, such as http://www.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016763.html

The "open browse vseries true" command worked for me too. Sorry for sending in the bug report.

Best,
Maria 


On 8/7/20, 12:32 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #3618: ChimeraX bug report submission
    ------------------------+-----------------------------
     Reporter:  mmaldo@…    |                Type:  defect
       Status:  new         |            Priority:  normal
    Component:  Unassigned  |          Blocked By:
     Blocking:              |  Notify when closed:
    ------------------------+-----------------------------
     {{{
     The following bug report has been submitted:
     Platform:        Darwin-18.7.0-x86_64-i386-64bit
     ChimeraX Version: 0.91 (2019-12-23)
     Description
     Hi,
     I've been getting a number of errors regarding the vseries command, mostly
     to do wit IndexError: list index out of range. I have a series of 20
     volumes. I'm not sure if this is a bug or if I'm not understanding the
     command properly. When I type "vseries play #1" I get no volume series
     specified, even though my volume series is #1 (#1.1-#1.20). Thank you.

     Log:
     UCSF ChimeraX version: 0.91 (2019-12-23)
     © 2016-2019 Regents of the University of California. All rights reserved.
     How to cite UCSF ChimeraX

     > open "/Users/mmaldo/Desktop/chimerax/200805 Session 39 3DVA-Rieske.cxs"
     > format session

     Summary of feedback from opening /Users/mmaldo/Desktop/chimerax/200805
     Session
     39 3DVA-Rieske.cxs
     ---
     warnings | restore_snapshot for "Volume" returned None
     restore_snapshot for "VolumeSurface" returned None
     notes | Error opening map "/Users/mmaldo/Desktop/chimerax/200805 Session
     39
     3DVA-Rieske.cxs": File 200805 Session 39 3DVA-Rieske.cxs, format mrc
     MRC header value nsymbt (-1334377196) is invalid

     opened ChimeraX session
     Traceback (most recent call last):
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/triggerset.py", line 130, in invoke
     return self._func(self._name, data)
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/model_panel/tool.py", line 158, in <lambda>
     lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
     parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
     IndexError: list index out of range

     Error processing trigger "new frame":
     IndexError: list index out of range

     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
     parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]

     See log for complete Python traceback.


     > open
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_019.mrc

     Opened FeS_frame_019.mrc, grid size 256,256,256, pixel 1.67, shown at
     level
     0.963, step 1, values float32
     Traceback (most recent call last):
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/triggerset.py", line 130, in invoke
     return self._func(self._name, data)
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/model_panel/tool.py", line 158, in <lambda>
     lambda *args, ft=self._fill_tree: ft(always_rebuild=True))
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
     parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]
     IndexError: list index out of range

     Error processing trigger "new frame":
     IndexError: list index out of range

     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/model_panel/tool.py", line 203, in _fill_tree
     parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]

     See log for complete Python traceback.


     > close session

     > open
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_000.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_019.mrc

     Opened FeS_frame_000.mrc, grid size 256,256,256, pixel 1.67, shown at
     level
     0.985, step 1, values float32

     > open
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/Vr_CIII2_fit_FeS_Ec1_QQ_nolipids-v2.pdb

     Chain information for Vr_CIII2_fit_FeS_Ec1_QQ_nolipids-v2.pdb #2
     ---
     Chain | Description
     A M | No description available
     B | No description available
     C | No description available
     D | No description available
     E | No description available
     F | No description available
     G S | No description available
     H | No description available
     J V | No description available
     K | No description available
     N | No description available
     O | No description available
     P | No description available
     Q | No description available
     R | No description available
     T | No description available
     W | No description available


     > open
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/Vr_CIII2_fit_Qc1_EQ_nolipids-v2.pdb

     Chain information for Vr_CIII2_fit_Qc1_EQ_nolipids-v2.pdb #3
     ---
     Chain | Description
     A M | No description available
     B | No description available
     C | No description available
     D | No description available
     E | No description available
     F | No description available
     G S | No description available
     H | No description available
     J V | No description available
     K | No description available
     N | No description available
     O | No description available
     P | No description available
     Q | No description available
     R | No description available
     T | No description available
     W | No description available


     > volume #1.1 level 1.106

     > volume #1.1 level 2.227

     > volume #1.1 level 2.1

     > volume #1.2 level 2.1

     > hide atoms

     > show cartoons

     > color sequential #1-2/A-K chains palette paired-10

     > color sequential #2-3/A-K chains palette paired-10

     > color sequential #2-3/M-W chains palette paired-10

     > hide #!1 models

     > show :hem :hec :hea :fes :zn :mg atoms

     > color byhetero

     Expected a keyword

     > select :hem :hec :hea :fes :zn :mg

     536 atoms, 568 bonds, 48 pseudobonds, 4 models selected

     > color sel byhetero

     > select clear

     > hide #!2 models

     > show #!2 models

     > hide #!3 models

     > view

     > morph #2,3

     Computed 21 frame morph #4

     > coordset #4 1,21

     > morph #2,3

     Computed 21 frame morph #5

     > coordset #5 1,21

     > movie record

     > movie encode /Users/mmaldo/Desktop/movie.mp4 framerate 25.0

     Movie saved to /Users/mmaldo/Desktop/movie.mp4


     > hide cartoons

     > ui mousemode rightMode select

     > hide sel atoms

     > hide sel atoms

     > show #1-2/C,D,Q cartoons

     > close #4

     > close #5

     > show #!2 models

     > show #!3 models

     > hide sel atoms

     > select up

     74 atoms, 64 bonds, 4 pseudobonds, 4 models selected

     > select up

     266 atoms, 284 bonds, 4 pseudobonds, 4 models selected

     > hide sel atoms

     > morph #2,3

     Computed 21 frame morph #4

     > coordset #4 1,21

     > save session "/Users/mmaldo/Desktop/chimerax/200806 Session 41 Rieske
     > morphs.cxs"

     > show #!1 models

     > hide #!1 models

     > show #!1 models

     > volume #1.1 level 2

     > volume #1.2 level 2

     > volume #1.1 level 1.8

     > turn y 180

     > turn y 180

     > turn y 90

     > turn y 90

     > turn y 90

     > turn y 90

     > volume #1.1 level 2

     > volume #1.1 level 1.8

     > volume #1.2 level 1.8

     > turn y 10

     > turn y -20

     > turn y 15

     > hide #!1 models

     > show #!1 models

     > hide #!1 models

     > show #!1 models

     > hide #!1 models

     > cofr #2/Q

     > cofr #2/Q

     > show #!1 models

     > view

     > view name front-full-CIII2

     > select #1.1

     2 models selected

     > select clear

     > ui mousemode rightMode translate

     > hide #!1 models

     > show #!1 models

     > hide #!1 models

     > show #!1 models

     > view name Rieske-zoom

     > view front-full-CIII2

     > view Rieske-zoom

     > hide #!1 models

     > open
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_001.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_002.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_003.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_004.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_005.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_006.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_007.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_008.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_009.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_010.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_011.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_012.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_013.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_014.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_015.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_016.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_017.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_018.mrc

     Opened FeS_frame_001.mrc, grid size 256,256,256, pixel 1.67, shown at
     level
     0.983, step 1, values float32

     > close #5

     > close #1

     > open
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_000.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_001.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_002.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_003.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_004.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_005.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_006.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_007.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_008.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_009.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_010.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_011.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_012.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_013.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_014.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_015.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_016.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_017.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_018.mrc
     >
     /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_019.mrc

     Opened FeS_frame_000.mrc, grid size 256,256,256, pixel 1.67, shown at
     level
     0.985, step 1, values float32

     > volume #1.1 level 1.8

     > volume #1.2 level 1.8

     > volume #1.5 level 1.8

     > volume #1.4 level 1.8

     > volume #1.3 level 1.8

     > volume #1.6 level 1.8

     > volume #1.7 level 1.8

     > volume #1.8 level 1.8

     > volume #1.10 level 1.8

     > volume #1.11 level 1.8

     > volume #1.12 level 1.8

     > volume #1.13 level 1.8

     > volume #1.15 level 1.8

     > volume #1.16 level 1.8

     > volume #1.14 level 1.8

     > volume #1.17 level 1.8

     > volume #1.18 level 1.8

     > volume #1.19 level 1.8

     > volume #1.20 level 1.8

     > volume #1.20 level 2.923

     > volume #1.20 level 1.8

     > hide #!1 models

     > show #!1 models

     > hide #!1.1 models

     > hide #!1.2 models

     > hide #!1.3 models

     > show #!1.3 models

     > hide #!1.4 models

     > hide #!1.3 models

     > hide #!1.5 models

     > hide #!1.6 models

     > hide #!1.7 models

     > hide #!1.8 models

     > hide #!1.9 models

     > hide #!1.10 models

     > hide #!1.11 models

     > hide #!1.12 models

     > hide #!1.13 models

     > hide #!1.14 models

     > hide #!1.15 models

     > hide #!1.16 models

     > hide #!1.17 models

     > hide #!1.18 models

     > hide #!1.19 models

     > hide #!1.20 models

     > show #!1.20 models

     > hide #!1.20 models

     > hide #!1 models

     > show #!1.1 models

     > hide #!1.1 models

     > show #!1.2 models

     > hide #!1.2 models

     > show #!1.3 models

     > hide #!1.3 models

     > show #!1.1 models

     > show #!1.20 models

     > hide #!1.1 models

     > hide #!4 models

     > vseries play #1

     No volume series specified

     > vseries play #1.1-1.20

     No volume series specified

     > vseries play #1 loop true

     No volume series specified

     > vseries play #1

     No volume series specified

     > vseries play #1.1

     No volume series specified

     > vseries play #1.1,1.20

     No volume series specified

     > vseries play #1.1

     No volume series specified

     > vseries play #1.1-1.20

     No volume series specified

     > vseries play #1.1-1.20

     No volume series specified

     Missing or invalid "series" argument: invalid map series specifier

     > vseries save #1 Rieske threshold 1.8

     Traceback (most recent call last):
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/cmd_line/tool.py", line 258, in execute
     cmd.run(cmd_text)
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/core/commands/cli.py", line 2837, in run
     result = ci.function(session, **kw_args)
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/map/series/vseries_command.py", line 189, in
     vseries_save
     s = series[0]
     IndexError: list index out of range

     IndexError: list index out of range

     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/map/series/vseries_command.py", line 189, in
     vseries_save
     s = series[0]

     See log for complete Python traceback.


     > vseries slider #1

     Traceback (most recent call last):
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/map/series/slider.py", line 142, in play_cb
     self.play()
     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/map/series/slider.py", line 148, in play
     s0 = ser[0]
     IndexError: list index out of range

     IndexError: list index out of range

     File
     "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
     packages/chimerax/map/series/slider.py", line 148, in play
     s0 = ser[0]

     See log for complete Python traceback.





     OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103
     OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine
     OpenGL vendor: NVIDIA Corporation

     }}}

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3618>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:4 by Eric Pettersen, 5 years ago

True, you do need to specify "vseries true" to the 'open' command. Nonetheless, a lot of the other errors that I see you encountered would be fixed by upgrading to 1.0. ;-)

--Eric

in reply to:  5 ; comment:5 by mmaldo@…, 5 years ago 

Thank you very much, Eric!

I get ChimeraX through SBGrid. I was assuming they keep it pretty updated. I'll download the 1.0 version directly.

Best,
Maria




On 8/7/20, 1:24 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #3618: vseries problems
    ----------------------------------+----------------------------
              Reporter:  mmaldo@…     |      Owner:  Eric Pettersen
                  Type:  defect       |     Status:  closed
              Priority:  normal       |  Milestone:
             Component:  Volume Data  |    Version:
            Resolution:  duplicate    |   Keywords:
            Blocked By:               |   Blocking:
    Notify when closed:               |   Platform:  all
               Project:  ChimeraX     |
    ----------------------------------+----------------------------

    Comment (by Eric Pettersen):

     True, you do need to specify "vseries true" to the 'open' command.
     Nonetheless, a lot of the other errors that I see you encountered would be
     fixed by upgrading to 1.0. ;-)

     --Eric

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3618#comment:4>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:6 by Eric Pettersen, 5 years ago

I suspect SBGrid hadn't updated because until a couple of days ago ISOLDE, a third-party plugin that a lot of people use, wasn't compatible with 1.0.

--Eric

in reply to:  7 ; comment:7 by mmaldo@…, 5 years ago 

AH! Good to know, that makes sense.

Thank you,
Maria

On 8/7/20, 2:57 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #3618: vseries problems
    ----------------------------------+----------------------------
              Reporter:  mmaldo@…     |      Owner:  Eric Pettersen
                  Type:  defect       |     Status:  closed
              Priority:  normal       |  Milestone:
             Component:  Volume Data  |    Version:
            Resolution:  duplicate    |   Keywords:
            Blocked By:               |   Blocking:
    Notify when closed:               |   Platform:  all
               Project:  ChimeraX     |
    ----------------------------------+----------------------------

    Comment (by Eric Pettersen):

     I suspect SBGrid hadn't updated because until a couple of days ago ISOLDE,
     a third-party plugin that a lot of people use, wasn't compatible with 1.0.

     --Eric

    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3618#comment:6>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
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